Back to Using R 4.1.3 to BUILD/CHECK a small subset of 3.18 packages |
This page was generated on 2024-03-08 16:41:48 -0500 (Fri, 08 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 655 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 59/118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
ggtree 3.10.1 (landing page) Guangchuang Yu
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ||||||||
To the developers/maintainers of the ggtree package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ggtree |
Version: 3.10.1 |
Command: /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings ggtree_3.10.1.tar.gz |
StartedAt: 2024-03-08 16:08:39 -0500 (Fri, 08 Mar 2024) |
EndedAt: 2024-03-08 16:09:49 -0500 (Fri, 08 Mar 2024) |
EllapsedTime: 70.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ggtree.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD check --install=check:ggtree.install-out.txt --library=/home/hpages/bbs-3.18-bioc-R41/R/site-library --timings ggtree_3.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/hpages/bbs-3.18-bioc-R41/meat/ggtree.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘ggtree/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ggtree’ version ‘3.10.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ggtree’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘ggtree.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
ggtree.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc-R41/R/bin/R CMD INSTALL ggtree ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-R41/R/site-library’ * installing *source* package ‘ggtree’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtree)
ggtree.Rcheck/tests/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ggtree) ggtree v3.10.1 For help: https://yulab-smu.top/treedata-book/ If you use the ggtree package suite in published research, please cite the appropriate paper(s): Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628 LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. doi: 10.1093/molbev/msz240 S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166 > > test_check("ggtree") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 14 ] > > proc.time() user system elapsed 2.296 0.140 2.426
ggtree.Rcheck/ggtree-Ex.timings
name | user | system | elapsed | |
attacher | 0.361 | 0.012 | 0.372 | |
collapse | 0.363 | 0.012 | 0.375 | |
expand | 0.121 | 0.035 | 0.156 | |
facet-plot | 0.185 | 0.008 | 0.194 | |
flip | 0.148 | 0.004 | 0.152 | |
geom-hilight | 1.603 | 0.004 | 1.607 | |
geom_balance | 0.219 | 0.000 | 0.218 | |
geom_cladelab | 0.366 | 0.008 | 0.374 | |
geom_label2 | 0.197 | 0.000 | 0.197 | |
geom_point2 | 0.821 | 0.008 | 0.829 | |
geom_rootedge | 0.709 | 0.044 | 0.753 | |
geom_rootpoint | 0.301 | 0.000 | 0.301 | |
geom_strip | 0.171 | 0.007 | 0.179 | |
geom_striplab | 0.199 | 0.001 | 0.199 | |
geom_tiplab | 0.151 | 0.000 | 0.151 | |
geom_tiplab2 | 0.302 | 0.000 | 0.302 | |
geom_tippoint | 0.215 | 0.000 | 0.216 | |
geom_tree | 0.187 | 0.000 | 0.187 | |
get_taxa_name | 0.038 | 0.004 | 0.042 | |
ggdensitree | 1.614 | 0.048 | 1.662 | |
ggexpand | 0.197 | 0.000 | 0.197 | |
ggtree-format-painter | 0.199 | 0.000 | 0.199 | |
ggtree | 0.204 | 0.000 | 0.204 | |
label_pad | 0.001 | 0.000 | 0.001 | |
open_tree | 0.266 | 0.000 | 0.265 | |
revts | 0.135 | 0.000 | 0.135 | |
rotate | 0.139 | 0.000 | 0.139 | |
rotate_tree | 0.205 | 0.000 | 0.206 | |
scaleClade | 0.33 | 0.00 | 0.33 | |
td_filter | 0.126 | 0.000 | 0.127 | |
theme_tree | 0.134 | 0.000 | 0.134 | |
theme_tree2 | 0.132 | 0.000 | 0.133 | |
tree-layout | 0.808 | 0.032 | 0.839 | |
viewClade | 0.179 | 0.000 | 0.179 | |
xlim_expand | 0.213 | 0.000 | 0.213 | |
xlim_tree | 0.227 | 0.000 | 0.227 | |
zoomClade | 0 | 0 | 0 | |